Wanshan is a city in southwest China that has several inactive mercury (Hg) mines. The local population are exposed to methylmercury (MeHg) due to the consumption of Hg contaminated rice. The relationship between Hg exposure and the cognitive functions of local children is unknown. This study investigated the relationship between hair Hg concentrations and the intelligence quotient (IQ) of 314 children aged 8–10 years, recruited from three local primary schools in Wanshan area in 2018 and 2019. IQ was evaluated using Wechsler Intelligence Scale for Children – Fourth Edition (WISC-IV). The average THg concentration in children's hair samples was 1.53 μg g⁻¹ (range: 0.21–12.6 μg g⁻¹), and 65.6% exceeded the United States Environment Protection Agency (USEPA) recommended value of 1 μg g⁻¹. Results of logistic regression analysis showed that children with hair Hg ≥ 1 μg g⁻¹ were 1.58 times more likely to have an IQ score <80, which is the clinical cut-off for borderline intellectual disability (R² = 0.20, p = 0.03). Increasing of 1 μg g⁻¹ hair Hg resulted in 1 point of IQ loss in Wanshan children, which was.much higher than that via fish consumption. The economical cost due to Hg exposure was estimated to be $69.8 million (9.43% of total GDP) in the Wanshan area in 2018.